The long-term goal of the proposed study is to provide a scientific basis to develop efficient primary prevention strategies against Helicobacter pylori (HP) associated morbidities, particularly gastric cancer, which remains the 2nd leading cause of cancer death and the 4th most commonly diagnosed cancer worldwide. Within the US, ethnic minorities, e.g., Asians, Blacks, Hispanics and Native Americans, experience an incidence almost twice as high as in non-Hispanic Whites. It is now clearly established that cagA and the type IV secretion system (T4SS) play a central role in the pathogenesis of HP-associated diseases. The cytotoxin-associated gene pathogenicity island (cagPAI) consists of a 40kb DNA region in the HP genome, and contains approximately 31 open reading frames, encoding cytotoxins and structural and functional components of the T4SS that acts as a molecular syringe injecting bacterial macromolecules into host cell cytosol. However, cagA status (a marker of cagPAI) alone is not sufficient to predict clinical outcomes in high risk populations where the majority of HP is cagA positive strains. Herein we hypothesize that cagPAI microvariability is an important determinant of cagA toxicity, leading to increased or reduced risk of high grade gastric precancerous and cancerous lesions. The proposed study will employ high throughput sequencing and genotyping technologies to gain knowledge of HP sequence variants associated with gastric histopathology. To date, high resolution single nucleotide polymorphisms (SNP) typing has rarely been used to classify specific pathogens, despite its widespread application to the human genome. The proposed study is aimed to extend our sustained successful international collaboration in studies on HP and gastrointestinal pathologies. We have demonstrated that the presence of cagA gene, marker of cytotoxin- associated gene pathogenicity island (cagPAI) has much greater impact on the risk of high grade premalignant lesions in comparison with host and environmental factors and identified possible cag gene microvariants that can alter the risk of gastric cancer drastically. Specifically we propose to validate our pilot observations concerning cagPAI genetic variants and gastric cancer by testing statistical associations with risk of cancer and high grade gastric precancerous lesions in large well characterized populations totaling more than 2000 individuals infected with cagA positive HP from both high and low risk Latin American countries. We will also expand this approach to additional cagPAI genes to discover new variants. Consequently this project will focus on cagA, cagC, cagE, cagI cagL, cagYc and cag Gamma, (a) whose functions have been well characterized in the model bacterial T4SS and/or (b) which are present extracellularly, suggesting possible interactions with host cells. We will investigate whether microvariants in the selected cagPAI genes are associated with gastric cancer risk or risk of high grade premalignant lesions, compared with the control group of the subjects who were not histologically diagnosed with gastric high grade premalignant lesions or cancer, and evaluate if the prevalence of those cagPAI microvariants are correlated with geographic variation in gastric cancer incidence within participating populations.